SC RNA-Seq: Checking for duplicates with dupRadar

Libraries required

Loading required package: viridisLite

Plotting and interpretation

The number of reads per base assigned to a gene in an ideal RNA-Seq data set is expected to be proportional to the abundance of its transcripts in the sample. For lowly expressed genes we expect read duplication to happen rarely by chance, while for highly expressed genes - depending on the total sequencing depth - we expect read duplication to happen often.

A good way to learn if a dataset is following this trend is by relating the normalized number of counts per gene (RPK, as a quantification of the gene expression) and the fraction represented by duplicated reads.

A duprate plot (blue cloud)

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Duprate Boxplot

The duprateExpBoxplot plot shows the range of the duplication rates at 5% bins (default) along the distribution of RPK gene counts. The x-axis displays the quantile of the RPK distribution, and the average RPK of the genes contained in this quantile.

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Adult_03

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Read counts expression

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Read counts expression histogram

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Comparison of multi-mapping RPK and uniquely-mapping RPK

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SessionInfo

─ Session info ──────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.6.1 (2019-07-05)
 os       Ubuntu 16.04.6 LTS          
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       Europe/Zurich               
 date     2019-08-19                  

─ Packages ──────────────────────────────────────────────────────────────
 package       * version   date       lib source        
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 assertthat      0.2.1     2019-03-21 [1] CRAN (R 3.6.1)
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 bitops          1.0-6     2013-08-17 [1] CRAN (R 3.6.1)
 blob            1.2.0     2019-07-09 [1] CRAN (R 3.6.1)
 bookdown        0.12      2019-07-11 [1] CRAN (R 3.6.1)
 callr           3.3.1     2019-07-18 [1] CRAN (R 3.6.1)
 cli             1.1.0     2019-03-19 [1] CRAN (R 3.6.1)
 colorspace      1.4-1     2019-03-18 [1] CRAN (R 3.6.1)
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 curl            4.0       2019-07-22 [1] CRAN (R 3.6.1)
 DBI             1.0.0     2018-05-02 [1] CRAN (R 3.6.1)
 desc            1.2.0     2018-05-01 [1] CRAN (R 3.6.1)
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[1] /home/ubuntu/R/x86_64-pc-linux-gnu-library/3.6
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library

Deepak Tanwar

Created on: 2019-08-16
Updated on: 2019-08-19